A previous study has shown effects of the New Nordic Diet (NND) to stimulate weight loss and lower systolic and diastolic blood pressure in obese Danish women and men in a randomized, controlled dietary intervention study. This work demonstrates long-term metabolic effects of the NND as compared to an Average Danish Diet (ADD) in blood plasma and reveals associations between metabolic changes and health beneficial effects of the NND including weight loss. A total of 145 individuals completed the intervention and blood samples were taken along with clinical examinations before the intervention started (week 0), and after 12 and 26 weeks. The plasma metabolome was measured using GC-MS and the final metabolite table contained 144 variables. Significant and novel metabolic effects of the diet, resulting weight loss, gender, and intervention study season were revealed using PLS-DA and ASCA. Several metabolites reflecting specific differences in the diets, especially intake of plant foods and seafood, and in energy metabolism related to ketone bodies and gluconeogenesis, formed the predominant metabolite pattern discriminating the intervention groups. Among NND subjects higher levels of vaccenic acid and 3-hydroxybutanoic acid were related to a higher weight loss, while higher concentrations of salicylic, lactic and N-aspartic acids, and 1,5-anhydro-D-sorbitol were related to a lower weight loss. Specific gender- and seasonal differences were also observed. The study strongly indicates that healthy diets high in fish, vegetables, fruit, and wholegrain facilitated weight loss and improved insulin sensitivity by increasing ketosis and gluconeogenesis in the fasting state.